Determining the effect of gene deletion is a fundamental approach to understanding gene
function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype …

Background We recently described FastTree, a tool for inferring phylogenies for alignments
with up to hundreds of thousands of sequences. Here, we describe improvements to …

Gene families are growing rapidly, but standard methods for inferring phylogenies do not
scale to alignments with over 10,000 sequences. We present FastTree, a method for …

Motivation: Molecular biotechnology now makes it possible to build elaborate systems
models, but the systems biology community needs information standards if models are to be …

Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating,
perturbing, and engineering cellular systems. Here, we develop a method for controlling gene …

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …

Noise has many roles in biological function, including generation of errors in DNA
replication leading to mutation and evolution, noise-driven divergence of cell fates, noise-induced …

Although similar integrative tools exist (Supplementary Note 2), no other open platform
shares all KBase’s features, which include the following:(i) comprehensive support for data …

Biological sensors can be engineered to measure a wide range of environmental conditions.
Here we show that statistical analysis of DNA from natural microbial communities can be …

Biochemical dynamics are often determined by series of single molecule events such as
gene expression and reactions involving protein concentrations at nanomolar concentrations. …